Skip to content

v1.2.0
Compare
Choose a tag to compare
@gbouras13 gbouras13 released this 24 Jan 06:29
· 340 commits to master since this release
v1.2.0
a58683a
This commit was created on GitHub.com and signed with GitHub’s verified signature. The key has expired.
GPG key ID: 4AEE18F83AFDEB23
Expired
Verified
Learn about vigilant mode.
  • Adds the functionality of matching each contig against the INPHARED database using mash (https://github.com/RyanCook94/inphared). The top hit for each contig (under a maximum mash distance threshold of 0.2) is kept.
  • New database adding INPHARED. You will need to re-download the pharokka database to use v1.2.0.
  • Replaced prodigal with pyrodigal as it is being actively maintained and used by bakta.
  • Adds --citation.
  • Adds checks for dependencies.
  • Adds --terminase terminase mode to re-orient a single contig phage to begin with a certain orientation and coordinate (most commonly, the large terminase subunit). With this, you must also specify --terminase_strand the strand of the terL gene and --terminase_start the start coordinate.
  • All locus tags end with 4 digits (trailing zeros) in order to play nice with vConTACT2 and start with 1 not 0.
  • In meta mode, the locus tags now begin with the contig header, not a random string (or chosen prefix).
  • Cleans up the .tbl so it should automatically be accepted by NCBI Bankit.
Assets 2
Loading